Open neuroniko opened 11 months ago
Hi, it is hard to say based on the error alone, but these a few possible issues it could be related to:
We have recently updated the tool and wrapper (CONIPHER v2.2.0), so I would recommend installing the latest conda environment and trying to rerun the analysis.
Dear TracerX team : I'd like to thank you for creating CONIPHER, it has been immensely useful in my work. I've been working with constructing tumour phylogenetic trees and came across an issue that I'm hoping you might be able to help me with. In most case, CONIPHER will work with this code: Rscript $Rscript_path --case_id ${case_id} --working_dir ${clustering_dir} --script_dir ${scriptDir} --input_tsv ${inputTSV} --clean_clusters TRUE --min_cluster_size 3 --nProc 1 However, in somes cases, after pyclone step, I encountered such error: Iteration: 9900 Number of clusters: 5 DP concentration: 707.759699054 Beta-Binomial precision: 912.87700996
PyClone build_table --config_file /public/workspace/guosy/project/WES/Wu_bam_file/LC_First/WuYY$ 105131_ZSX_TP/CONIPHER/1.Clustering//Wu_YY_2105131_ZSX_TP_cluster9//Wu_YY_2105131_ZSX_TP_cluster9$ config.yaml --table_type old_style --out_file /public/workspace/guosy/project/WES/Wu_bamfile/LC$ irst/Wu_YY_2105131_ZSX_TP/CONIPHER/1.Clustering//Wu_YY_2105131_ZSX_TP_cluster9//Wu_YY_2105131_ZSX$ TP.results.tsv --max_clusters 1 --burnin 1000 Error in simpleClusterList[[as.character(ITH1clust)]] : attempt to select less than one element in get1index Execution halted
Any guidance or suggestions would be greatly appreciated.
Thank you for your time and your contribution to the CONIPHER.